2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.api.AlignViewportI;
24 import jalview.bin.Cache;
25 import jalview.commands.EditCommand;
26 import jalview.commands.EditCommand.Action;
27 import jalview.commands.EditCommand.Edit;
28 import jalview.datamodel.AlignmentI;
29 import jalview.datamodel.ColumnSelection;
30 import jalview.datamodel.HiddenColumns;
31 import jalview.datamodel.SearchResultMatchI;
32 import jalview.datamodel.SearchResults;
33 import jalview.datamodel.SearchResultsI;
34 import jalview.datamodel.Sequence;
35 import jalview.datamodel.SequenceFeature;
36 import jalview.datamodel.SequenceGroup;
37 import jalview.datamodel.SequenceI;
38 import jalview.io.SequenceAnnotationReport;
39 import jalview.renderer.ResidueShaderI;
40 import jalview.schemes.ResidueProperties;
41 import jalview.structure.SelectionListener;
42 import jalview.structure.SelectionSource;
43 import jalview.structure.SequenceListener;
44 import jalview.structure.StructureSelectionManager;
45 import jalview.structure.VamsasSource;
46 import jalview.util.Comparison;
47 import jalview.util.MappingUtils;
48 import jalview.util.MessageManager;
49 import jalview.util.Platform;
50 import jalview.viewmodel.AlignmentViewport;
52 import java.awt.BorderLayout;
53 import java.awt.Color;
55 import java.awt.FontMetrics;
56 import java.awt.Point;
57 import java.awt.event.MouseEvent;
58 import java.awt.event.MouseListener;
59 import java.awt.event.MouseMotionListener;
60 import java.awt.event.MouseWheelEvent;
61 import java.awt.event.MouseWheelListener;
62 import java.util.ArrayList;
63 import java.util.Collections;
64 import java.util.List;
65 import java.util.ListIterator;
67 import javax.swing.JPanel;
68 import javax.swing.SwingUtilities;
69 import javax.swing.ToolTipManager;
75 * @version $Revision: 1.130 $
77 public class SeqPanel extends JPanel
78 implements MouseListener, MouseMotionListener, MouseWheelListener,
79 SequenceListener, SelectionListener
83 public SeqCanvas seqCanvas;
86 public AlignmentPanel ap;
88 protected int lastres;
90 protected int startseq;
92 protected AlignViewport av;
94 ScrollThread scrollThread = null;
96 boolean mouseDragging = false;
98 boolean editingSeqs = false;
100 boolean groupEditing = false;
102 // ////////////////////////////////////////
103 // ///Everything below this is for defining the boundary of the rubberband
104 // ////////////////////////////////////////
107 boolean changeEndSeq = false;
109 boolean changeStartSeq = false;
111 boolean changeEndRes = false;
113 boolean changeStartRes = false;
115 SequenceGroup stretchGroup = null;
117 boolean remove = false;
119 Point lastMousePress;
121 boolean mouseWheelPressed = false;
123 StringBuffer keyboardNo1;
125 StringBuffer keyboardNo2;
127 java.net.URL linkImageURL;
129 private final SequenceAnnotationReport seqARep;
131 StringBuilder tooltipText = new StringBuilder();
135 EditCommand editCommand;
137 StructureSelectionManager ssm;
139 SearchResultsI lastSearchResults;
142 * Creates a new SeqPanel object.
149 public SeqPanel(AlignViewport av, AlignmentPanel ap)
151 linkImageURL = getClass().getResource("/images/link.gif");
152 seqARep = new SequenceAnnotationReport(linkImageURL.toString());
153 ToolTipManager.sharedInstance().registerComponent(this);
154 ToolTipManager.sharedInstance().setInitialDelay(0);
155 ToolTipManager.sharedInstance().setDismissDelay(10000);
157 setBackground(Color.white);
159 seqCanvas = new SeqCanvas(ap);
160 setLayout(new BorderLayout());
161 add(seqCanvas, BorderLayout.CENTER);
167 addMouseMotionListener(this);
168 addMouseListener(this);
169 addMouseWheelListener(this);
170 ssm = av.getStructureSelectionManager();
171 ssm.addStructureViewerListener(this);
172 ssm.addSelectionListener(this);
176 int startWrapBlock = -1;
178 int wrappedBlock = -1;
181 * Returns the aligned sequence position (base 0) at the mouse position, or
182 * the closest visible one
187 int findColumn(MouseEvent evt)
192 int startRes = av.getRanges().getStartRes();
193 if (av.getWrapAlignment())
196 int hgap = av.getCharHeight();
197 if (av.getScaleAboveWrapped())
199 hgap += av.getCharHeight();
202 int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
203 + hgap + seqCanvas.getAnnotationHeight();
207 x = Math.max(0, x - seqCanvas.LABEL_WEST);
209 int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
215 wrappedBlock = y / cHeight;
216 wrappedBlock += startRes / cwidth;
217 // allow for wrapped view scrolled right (possible from Overview)
218 int startOffset = startRes % cwidth;
219 res = wrappedBlock * cwidth + startOffset
220 + +Math.min(cwidth - 1, x / av.getCharWidth());
224 if (x > seqCanvas.getX() + seqCanvas.getWidth())
226 // make sure we calculate relative to visible alignment, rather than
228 x = seqCanvas.getX() + seqCanvas.getWidth();
230 res = (x / av.getCharWidth()) + startRes;
231 if (res > av.getRanges().getEndRes())
234 res = av.getRanges().getEndRes();
238 if (av.hasHiddenColumns())
240 res = av.getAlignment().getHiddenColumns()
241 .adjustForHiddenColumns(res);
248 int findSeq(MouseEvent evt)
253 if (av.getWrapAlignment())
255 int hgap = av.getCharHeight();
256 if (av.getScaleAboveWrapped())
258 hgap += av.getCharHeight();
261 int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
262 + hgap + seqCanvas.getAnnotationHeight();
266 seq = Math.min((y % cHeight) / av.getCharHeight(),
267 av.getAlignment().getHeight() - 1);
272 (y / av.getCharHeight()) + av.getRanges().getStartSeq(),
273 av.getAlignment().getHeight() - 1);
280 * When all of a sequence of edits are complete, put the resulting edit list
281 * on the history stack (undo list), and reset flags for editing in progress.
287 if (editCommand != null && editCommand.getSize() > 0)
289 ap.alignFrame.addHistoryItem(editCommand);
290 av.firePropertyChange("alignment", null,
291 av.getAlignment().getSequences());
296 * Tidy up come what may...
301 groupEditing = false;
310 seqCanvas.cursorY = getKeyboardNo1() - 1;
314 void setCursorColumn()
316 seqCanvas.cursorX = getKeyboardNo1() - 1;
320 void setCursorRowAndColumn()
322 if (keyboardNo2 == null)
324 keyboardNo2 = new StringBuffer();
328 seqCanvas.cursorX = getKeyboardNo1() - 1;
329 seqCanvas.cursorY = getKeyboardNo2() - 1;
334 void setCursorPosition()
336 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
338 seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
342 void moveCursor(int dx, int dy)
344 seqCanvas.cursorX += dx;
345 seqCanvas.cursorY += dy;
347 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
349 if (av.hasHiddenColumns() && !hidden.isVisible(seqCanvas.cursorX))
351 int original = seqCanvas.cursorX - dx;
352 int maxWidth = av.getAlignment().getWidth();
354 while (!hidden.isVisible(seqCanvas.cursorX)
355 && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
357 seqCanvas.cursorX += dx;
360 if (seqCanvas.cursorX >= maxWidth
361 || !hidden.isVisible(seqCanvas.cursorX))
363 seqCanvas.cursorX = original;
370 void scrollToVisible()
372 if (seqCanvas.cursorX < 0)
374 seqCanvas.cursorX = 0;
376 else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1)
378 seqCanvas.cursorX = av.getAlignment().getWidth() - 1;
381 if (seqCanvas.cursorY < 0)
383 seqCanvas.cursorY = 0;
385 else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1)
387 seqCanvas.cursorY = av.getAlignment().getHeight() - 1;
391 if (av.getWrapAlignment())
393 av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX);
397 av.getRanges().scrollToVisible(seqCanvas.cursorX, seqCanvas.cursorY);
399 setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
400 seqCanvas.cursorX, seqCanvas.cursorY);
405 void setSelectionAreaAtCursor(boolean topLeft)
407 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
409 if (av.getSelectionGroup() != null)
411 SequenceGroup sg = av.getSelectionGroup();
412 // Find the top and bottom of this group
413 int min = av.getAlignment().getHeight(), max = 0;
414 for (int i = 0; i < sg.getSize(); i++)
416 int index = av.getAlignment().findIndex(sg.getSequenceAt(i));
431 sg.setStartRes(seqCanvas.cursorX);
432 if (sg.getEndRes() < seqCanvas.cursorX)
434 sg.setEndRes(seqCanvas.cursorX);
437 min = seqCanvas.cursorY;
441 sg.setEndRes(seqCanvas.cursorX);
442 if (sg.getStartRes() > seqCanvas.cursorX)
444 sg.setStartRes(seqCanvas.cursorX);
447 max = seqCanvas.cursorY + 1;
452 // Only the user can do this
453 av.setSelectionGroup(null);
457 // Now add any sequences between min and max
458 sg.getSequences(null).clear();
459 for (int i = min; i < max; i++)
461 sg.addSequence(av.getAlignment().getSequenceAt(i), false);
466 if (av.getSelectionGroup() == null)
468 SequenceGroup sg = new SequenceGroup();
469 sg.setStartRes(seqCanvas.cursorX);
470 sg.setEndRes(seqCanvas.cursorX);
471 sg.addSequence(sequence, false);
472 av.setSelectionGroup(sg);
475 ap.paintAlignment(false);
479 void insertGapAtCursor(boolean group)
481 groupEditing = group;
482 startseq = seqCanvas.cursorY;
483 lastres = seqCanvas.cursorX;
484 editSequence(true, false, seqCanvas.cursorX + getKeyboardNo1());
488 void deleteGapAtCursor(boolean group)
490 groupEditing = group;
491 startseq = seqCanvas.cursorY;
492 lastres = seqCanvas.cursorX + getKeyboardNo1();
493 editSequence(false, false, seqCanvas.cursorX);
497 void insertNucAtCursor(boolean group, String nuc)
499 // TODO not called - delete?
500 groupEditing = group;
501 startseq = seqCanvas.cursorY;
502 lastres = seqCanvas.cursorX;
503 editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1());
507 void numberPressed(char value)
509 if (keyboardNo1 == null)
511 keyboardNo1 = new StringBuffer();
514 if (keyboardNo2 != null)
516 keyboardNo2.append(value);
520 keyboardNo1.append(value);
528 if (keyboardNo1 != null)
530 int value = Integer.parseInt(keyboardNo1.toString());
534 } catch (Exception x)
545 if (keyboardNo2 != null)
547 int value = Integer.parseInt(keyboardNo2.toString());
551 } catch (Exception x)
565 public void mouseReleased(MouseEvent evt)
567 boolean didDrag = mouseDragging; // did we come here after a drag
568 mouseDragging = false;
569 mouseWheelPressed = false;
571 if (evt.isPopupTrigger()) // Windows: mouseReleased
580 doMouseReleasedDefineMode(evt, didDrag);
594 public void mousePressed(MouseEvent evt)
596 lastMousePress = evt.getPoint();
598 if (SwingUtilities.isMiddleMouseButton(evt))
600 mouseWheelPressed = true;
604 boolean isControlDown = Platform.isControlDown(evt);
605 if (evt.isShiftDown() || isControlDown)
615 doMousePressedDefineMode(evt);
619 int seq = findSeq(evt);
620 int res = findColumn(evt);
622 if (seq < 0 || res < 0)
627 if ((seq < av.getAlignment().getHeight())
628 && (res < av.getAlignment().getSequenceAt(seq).getLength()))
645 public void mouseOverSequence(SequenceI sequence, int index, int pos)
647 String tmp = sequence.hashCode() + " " + index + " " + pos;
649 if (lastMessage == null || !lastMessage.equals(tmp))
651 // System.err.println("mouseOver Sequence: "+tmp);
652 ssm.mouseOverSequence(sequence, index, pos, av);
658 * Highlight the mapped region described by the search results object (unless
659 * unchanged). This supports highlight of protein while mousing over linked
660 * cDNA and vice versa. The status bar is also updated to show the location of
661 * the start of the highlighted region.
664 public void highlightSequence(SearchResultsI results)
666 if (results == null || results.equals(lastSearchResults))
670 lastSearchResults = results;
672 if (av.isFollowHighlight())
674 // don't allow highlight of protein/cDNA to also scroll a complementary
675 // panel,as this sets up a feedback loop (scrolling panel 1 causes moused
676 // over residue to change abruptly, causing highlighted residue in panel 2
677 // to change, causing a scroll in panel 1 etc)
678 ap.setToScrollComplementPanel(false);
679 if (ap.scrollToPosition(results, false))
681 seqCanvas.revalidate();
683 ap.setToScrollComplementPanel(true);
685 setStatusMessage(results);
686 seqCanvas.highlightSearchResults(results);
690 public VamsasSource getVamsasSource()
692 return this.ap == null ? null : this.ap.av;
696 public void updateColours(SequenceI seq, int index)
698 System.out.println("update the seqPanel colours");
709 public void mouseMoved(MouseEvent evt)
713 // This is because MacOSX creates a mouseMoved
714 // If control is down, other platforms will not.
718 final int column = findColumn(evt);
719 int seq = findSeq(evt);
720 if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
725 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
727 if (column >= sequence.getLength())
733 * set status bar message, returning residue position in sequence
735 boolean isGapped = Comparison.isGap(sequence.getCharAt(column));
736 final int pos = setStatusMessage(sequence, column, seq);
737 if (ssm != null && !isGapped)
739 mouseOverSequence(sequence, column, pos);
742 tooltipText.setLength(6); // Cuts the buffer back to <html>
744 SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
747 for (int g = 0; g < groups.length; g++)
749 if (groups[g].getStartRes() <= column
750 && groups[g].getEndRes() >= column)
752 if (!groups[g].getName().startsWith("JTreeGroup")
753 && !groups[g].getName().startsWith("JGroup"))
755 tooltipText.append(groups[g].getName());
758 if (groups[g].getDescription() != null)
760 tooltipText.append(": " + groups[g].getDescription());
767 * add any features at the position to the tooltip; if over a gap, only
768 * add features that straddle the gap (pos may be the residue before or
771 if (av.isShowSequenceFeatures())
773 List<SequenceFeature> features = ap.getFeatureRenderer()
774 .findFeaturesAtRes(sequence.getDatasetSequence(), pos);
777 removeAdjacentFeatures(features, column + 1, sequence);
779 seqARep.appendFeatures(tooltipText, pos, features,
780 this.ap.getSeqPanel().seqCanvas.fr.getMinMax());
782 if (tooltipText.length() == 6) // <html>
784 setToolTipText(null);
789 if (lastTooltip == null
790 || !lastTooltip.equals(tooltipText.toString()))
792 String formatedTooltipText = JvSwingUtils.wrapTooltip(true,
793 tooltipText.toString());
794 // String formatedTooltipText = tooltipText.toString();
795 setToolTipText(formatedTooltipText);
796 lastTooltip = tooltipText.toString();
804 * Removes from the list of features any that start after, or end before, the
805 * given column position. This allows us to retain only those features
806 * adjacent to a gapped position that straddle the position. Contact features
807 * that 'straddle' the position are also removed, since they are not 'at' the
812 * alignment column (1..)
815 protected void removeAdjacentFeatures(List<SequenceFeature> features,
816 final int column, SequenceI sequence)
818 // TODO should this be an AlignViewController method (and reused by applet)?
819 ListIterator<SequenceFeature> it = features.listIterator();
822 SequenceFeature sf = it.next();
823 if (sf.isContactFeature()
824 || sequence.findIndex(sf.getBegin()) > column
825 || sequence.findIndex(sf.getEnd()) < column)
832 private Point lastp = null;
837 * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent)
840 public Point getToolTipLocation(MouseEvent event)
842 int x = event.getX(), w = getWidth();
843 int wdth = (w - x < 200) ? -(w / 2) : 5; // switch sides when tooltip is too
846 if (!event.isShiftDown() || p == null)
848 p = (tooltipText != null && tooltipText.length() > 6)
849 ? new Point(event.getX() + wdth, event.getY() - 20)
853 * TODO: try to modify position region is not obcured by tooltip
861 * set when the current UI interaction has resulted in a change that requires
862 * overview shading to be recalculated. this could be changed to something
863 * more expressive that indicates what actually has changed, so selective
864 * redraws can be applied
866 private boolean needOverviewUpdate = false; // TODO: refactor to avcontroller
869 * set if av.getSelectionGroup() refers to a group that is defined on the
870 * alignment view, rather than a transient selection
872 // private boolean editingDefinedGroup = false; // TODO: refactor to
873 // avcontroller or viewModel
876 * Sets the status message in alignment panel, showing the sequence number
877 * (index) and id, and residue and residue position if not at a gap, for the
878 * given sequence and column position. Returns the residue position returned
879 * by Sequence.findPosition. Note this may be for the nearest adjacent residue
880 * if at a gapped position.
883 * aligned sequence object
887 * index of sequence in alignment
888 * @return sequence position of residue at column, or adjacent residue if at a
891 int setStatusMessage(SequenceI sequence, final int column, int seq)
893 StringBuilder text = new StringBuilder(32);
896 * Sequence number (if known), and sequence name.
898 String seqno = seq == -1 ? "" : " " + (seq + 1);
899 text.append("Sequence").append(seqno).append(" ID: ")
900 .append(sequence.getName());
902 String residue = null;
905 * Try to translate the display character to residue name (null for gap).
907 final String displayChar = String.valueOf(sequence.getCharAt(column));
908 boolean isGapped = Comparison.isGap(sequence.getCharAt(column));
909 int pos = sequence.findPosition(column);
913 boolean nucleotide = av.getAlignment().isNucleotide();
916 residue = ResidueProperties.nucleotideName.get(displayChar);
920 residue = "X".equalsIgnoreCase(displayChar) ? "X"
921 : ("*".equals(displayChar) ? "STOP"
922 : ResidueProperties.aa2Triplet.get(displayChar));
924 text.append(" ").append(nucleotide ? "Nucleotide" : "Residue")
925 .append(": ").append(residue == null ? displayChar : residue);
927 text.append(" (").append(Integer.toString(pos)).append(")");
929 ap.alignFrame.statusBar.setText(text.toString());
935 * Set the status bar message to highlight the first matched position in
940 private void setStatusMessage(SearchResultsI results)
942 AlignmentI al = this.av.getAlignment();
943 int sequenceIndex = al.findIndex(results);
944 if (sequenceIndex == -1)
948 SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
949 for (SearchResultMatchI m : results.getResults())
951 SequenceI seq = m.getSequence();
952 if (seq.getDatasetSequence() != null)
954 seq = seq.getDatasetSequence();
960 * Convert position in sequence (base 1) to sequence character array
963 int start = m.getStart() - m.getSequence().getStart();
964 setStatusMessage(seq, start, sequenceIndex);
974 public void mouseDragged(MouseEvent evt)
976 if (mouseWheelPressed)
978 boolean inSplitFrame = ap.av.getCodingComplement() != null;
979 boolean copyChanges = inSplitFrame && av.isProteinFontAsCdna();
981 int oldWidth = av.getCharWidth();
983 // Which is bigger, left-right or up-down?
984 if (Math.abs(evt.getY() - lastMousePress.getY()) > Math
985 .abs(evt.getX() - lastMousePress.getX()))
988 * on drag up or down, decrement or increment font size
990 int fontSize = av.font.getSize();
991 boolean fontChanged = false;
993 if (evt.getY() < lastMousePress.getY())
998 else if (evt.getY() > lastMousePress.getY())
1011 Font newFont = new Font(av.font.getName(), av.font.getStyle(),
1013 av.setFont(newFont, true);
1014 av.setCharWidth(oldWidth);
1018 ap.av.getCodingComplement().setFont(newFont, true);
1019 SplitFrame splitFrame = (SplitFrame) ap.alignFrame
1020 .getSplitViewContainer();
1021 splitFrame.adjustLayout();
1022 splitFrame.repaint();
1029 * on drag left or right, decrement or increment character width
1032 if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1)
1034 newWidth = av.getCharWidth() - 1;
1035 av.setCharWidth(newWidth);
1037 else if (evt.getX() > lastMousePress.getX())
1039 newWidth = av.getCharWidth() + 1;
1040 av.setCharWidth(newWidth);
1044 ap.paintAlignment(false);
1048 * need to ensure newWidth is set on cdna, regardless of which
1049 * panel the mouse drag happened in; protein will compute its
1050 * character width as 1:1 or 3:1
1052 av.getCodingComplement().setCharWidth(newWidth);
1053 SplitFrame splitFrame = (SplitFrame) ap.alignFrame
1054 .getSplitViewContainer();
1055 splitFrame.adjustLayout();
1056 splitFrame.repaint();
1061 FontMetrics fm = getFontMetrics(av.getFont());
1062 av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
1064 lastMousePress = evt.getPoint();
1071 doMouseDraggedDefineMode(evt);
1075 int res = findColumn(evt);
1082 if ((lastres == -1) || (lastres == res))
1087 if ((res < av.getAlignment().getWidth()) && (res < lastres))
1089 // dragLeft, delete gap
1090 editSequence(false, false, res);
1094 editSequence(true, false, res);
1097 mouseDragging = true;
1098 if ((scrollThread != null) && (scrollThread.isRunning()))
1100 scrollThread.setEvent(evt);
1104 // TODO: Make it more clever than many booleans
1105 synchronized void editSequence(boolean insertGap, boolean editSeq,
1109 int fixedRight = -1;
1110 boolean fixedColumns = false;
1111 SequenceGroup sg = av.getSelectionGroup();
1113 SequenceI seq = av.getAlignment().getSequenceAt(startseq);
1115 // No group, but the sequence may represent a group
1116 if (!groupEditing && av.hasHiddenRows())
1118 if (av.isHiddenRepSequence(seq))
1120 sg = av.getRepresentedSequences(seq);
1121 groupEditing = true;
1125 StringBuilder message = new StringBuilder(64);
1128 message.append("Edit group:");
1129 if (editCommand == null)
1131 editCommand = new EditCommand(
1132 MessageManager.getString("action.edit_group"));
1137 message.append("Edit sequence: " + seq.getName());
1138 String label = seq.getName();
1139 if (label.length() > 10)
1141 label = label.substring(0, 10);
1143 if (editCommand == null)
1145 editCommand = new EditCommand(MessageManager
1146 .formatMessage("label.edit_params", new String[]
1153 message.append(" insert ");
1157 message.append(" delete ");
1160 message.append(Math.abs(startres - lastres) + " gaps.");
1161 ap.alignFrame.statusBar.setText(message.toString());
1163 // Are we editing within a selection group?
1164 if (groupEditing || (sg != null
1165 && sg.getSequences(av.getHiddenRepSequences()).contains(seq)))
1167 fixedColumns = true;
1169 // sg might be null as the user may only see 1 sequence,
1170 // but the sequence represents a group
1173 if (!av.isHiddenRepSequence(seq))
1178 sg = av.getRepresentedSequences(seq);
1181 fixedLeft = sg.getStartRes();
1182 fixedRight = sg.getEndRes();
1184 if ((startres < fixedLeft && lastres >= fixedLeft)
1185 || (startres >= fixedLeft && lastres < fixedLeft)
1186 || (startres > fixedRight && lastres <= fixedRight)
1187 || (startres <= fixedRight && lastres > fixedRight))
1193 if (fixedLeft > startres)
1195 fixedRight = fixedLeft - 1;
1198 else if (fixedRight < startres)
1200 fixedLeft = fixedRight;
1205 if (av.hasHiddenColumns())
1207 fixedColumns = true;
1208 int y1 = av.getAlignment().getHiddenColumns()
1209 .getHiddenBoundaryLeft(startres);
1210 int y2 = av.getAlignment().getHiddenColumns()
1211 .getHiddenBoundaryRight(startres);
1213 if ((insertGap && startres > y1 && lastres < y1)
1214 || (!insertGap && startres < y2 && lastres > y2))
1220 // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
1221 // Selection spans a hidden region
1222 if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
1230 fixedRight = y2 - 1;
1237 List<SequenceI> vseqs = sg.getSequences(av.getHiddenRepSequences());
1238 int g, groupSize = vseqs.size();
1239 SequenceI[] groupSeqs = new SequenceI[groupSize];
1240 for (g = 0; g < groupSeqs.length; g++)
1242 groupSeqs[g] = vseqs.get(g);
1248 // If the user has selected the whole sequence, and is dragging to
1249 // the right, we can still extend the alignment and selectionGroup
1250 if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
1251 && sg.getEndRes() == av.getAlignment().getWidth() - 1)
1253 sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);
1254 fixedRight = sg.getEndRes();
1257 // Is it valid with fixed columns??
1258 // Find the next gap before the end
1259 // of the visible region boundary
1260 boolean blank = false;
1261 for (fixedRight = fixedRight; fixedRight > lastres; fixedRight--)
1265 for (g = 0; g < groupSize; g++)
1267 for (int j = 0; j < startres - lastres; j++)
1269 if (!Comparison.isGap(groupSeqs[g].getCharAt(fixedRight - j)))
1284 if (sg.getSize() == av.getAlignment().getHeight())
1286 if ((av.hasHiddenColumns() && startres < av.getAlignment()
1287 .getHiddenColumns().getHiddenBoundaryRight(startres)))
1293 int alWidth = av.getAlignment().getWidth();
1294 if (av.hasHiddenRows())
1296 int hwidth = av.getAlignment().getHiddenSequences()
1298 if (hwidth > alWidth)
1303 // We can still insert gaps if the selectionGroup
1304 // contains all the sequences
1305 sg.setEndRes(sg.getEndRes() + startres - lastres);
1306 fixedRight = alWidth + startres - lastres;
1317 else if (!insertGap)
1319 // / Are we able to delete?
1320 // ie are all columns blank?
1322 for (g = 0; g < groupSize; g++)
1324 for (int j = startres; j < lastres; j++)
1326 if (groupSeqs[g].getLength() <= j)
1331 if (!Comparison.isGap(groupSeqs[g].getCharAt(j)))
1333 // Not a gap, block edit not valid
1343 // dragging to the right
1344 if (fixedColumns && fixedRight != -1)
1346 for (int j = lastres; j < startres; j++)
1348 insertChar(j, groupSeqs, fixedRight);
1353 appendEdit(Action.INSERT_GAP, groupSeqs, startres,
1354 startres - lastres);
1359 // dragging to the left
1360 if (fixedColumns && fixedRight != -1)
1362 for (int j = lastres; j > startres; j--)
1364 deleteChar(startres, groupSeqs, fixedRight);
1369 appendEdit(Action.DELETE_GAP, groupSeqs, startres,
1370 lastres - startres);
1376 // ///Editing a single sequence///////////
1380 // dragging to the right
1381 if (fixedColumns && fixedRight != -1)
1383 for (int j = lastres; j < startres; j++)
1385 insertChar(j, new SequenceI[] { seq }, fixedRight);
1390 appendEdit(Action.INSERT_GAP, new SequenceI[] { seq }, lastres,
1391 startres - lastres);
1398 // dragging to the left
1399 if (fixedColumns && fixedRight != -1)
1401 for (int j = lastres; j > startres; j--)
1403 if (!Comparison.isGap(seq.getCharAt(startres)))
1408 deleteChar(startres, new SequenceI[] { seq }, fixedRight);
1413 // could be a keyboard edit trying to delete none gaps
1415 for (int m = startres; m < lastres; m++)
1417 if (!Comparison.isGap(seq.getCharAt(m)))
1426 appendEdit(Action.DELETE_GAP, new SequenceI[] { seq },
1432 {// insertGap==false AND editSeq==TRUE;
1433 if (fixedColumns && fixedRight != -1)
1435 for (int j = lastres; j < startres; j++)
1437 insertChar(j, new SequenceI[] { seq }, fixedRight);
1442 appendEdit(Action.INSERT_NUC, new SequenceI[] { seq }, lastres,
1443 startres - lastres);
1450 seqCanvas.repaint();
1453 void insertChar(int j, SequenceI[] seq, int fixedColumn)
1455 int blankColumn = fixedColumn;
1456 for (int s = 0; s < seq.length; s++)
1458 // Find the next gap before the end of the visible region boundary
1459 // If lastCol > j, theres a boundary after the gap insertion
1461 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
1463 if (Comparison.isGap(seq[s].getCharAt(blankColumn)))
1465 // Theres a space, so break and insert the gap
1470 if (blankColumn <= j)
1472 blankColumn = fixedColumn;
1478 appendEdit(Action.DELETE_GAP, seq, blankColumn, 1);
1480 appendEdit(Action.INSERT_GAP, seq, j, 1);
1485 * Helper method to add and perform one edit action.
1492 protected void appendEdit(Action action, SequenceI[] seq, int pos,
1496 final Edit edit = new EditCommand().new Edit(action, seq, pos, count,
1497 av.getAlignment().getGapCharacter());
1499 editCommand.appendEdit(edit, av.getAlignment(), true, null);
1502 void deleteChar(int j, SequenceI[] seq, int fixedColumn)
1505 appendEdit(Action.DELETE_GAP, seq, j, 1);
1507 appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1);
1517 public void mouseEntered(MouseEvent e)
1524 if ((scrollThread != null) && (scrollThread.isRunning()))
1526 scrollThread.stopScrolling();
1527 scrollThread = null;
1538 public void mouseExited(MouseEvent e)
1540 if (av.getWrapAlignment())
1545 if (mouseDragging && scrollThread == null)
1547 scrollThread = new ScrollThread();
1552 * Handler for double-click on a position with one or more sequence features.
1553 * Opens the Amend Features dialog to allow feature details to be amended, or
1554 * the feature deleted.
1557 public void mouseClicked(MouseEvent evt)
1559 SequenceGroup sg = null;
1560 SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
1561 if (evt.getClickCount() > 1)
1563 sg = av.getSelectionGroup();
1564 if (sg != null && sg.getSize() == 1
1565 && sg.getEndRes() - sg.getStartRes() < 2)
1567 av.setSelectionGroup(null);
1570 int column = findColumn(evt);
1571 boolean isGapped = Comparison.isGap(sequence.getCharAt(column));
1574 * find features at the position (if not gapped), or straddling
1575 * the position (if at a gap)
1577 List<SequenceFeature> features = seqCanvas.getFeatureRenderer()
1578 .findFeaturesAtRes(sequence.getDatasetSequence(),
1579 sequence.findPosition(column));
1582 removeAdjacentFeatures(features, column, sequence);
1585 if (!features.isEmpty())
1588 * highlight the first feature at the position on the alignment
1590 SearchResultsI highlight = new SearchResults();
1591 highlight.addResult(sequence, features.get(0).getBegin(),
1592 features.get(0).getEnd());
1593 seqCanvas.highlightSearchResults(highlight);
1596 * open the Amend Features dialog; clear highlighting afterwards,
1597 * whether changes were made or not
1599 List<SequenceI> seqs = Collections.singletonList(sequence);
1600 seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false,
1602 seqCanvas.highlightSearchResults(null);
1608 public void mouseWheelMoved(MouseWheelEvent e)
1611 if (e.getWheelRotation() > 0)
1613 if (e.isShiftDown())
1615 av.getRanges().scrollRight(true);
1618 else if (!av.getWrapAlignment())
1620 av.getRanges().scrollUp(false);
1625 if (e.isShiftDown())
1627 av.getRanges().scrollRight(false);
1629 else if (!av.getWrapAlignment())
1631 av.getRanges().scrollUp(true);
1634 // TODO Update tooltip for new position.
1643 public void doMousePressedDefineMode(MouseEvent evt)
1645 final int res = findColumn(evt);
1646 final int seq = findSeq(evt);
1648 needOverviewUpdate = false;
1650 startWrapBlock = wrappedBlock;
1652 if (av.getWrapAlignment() && seq > av.getAlignment().getHeight())
1654 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1655 MessageManager.getString(
1656 "label.cannot_edit_annotations_in_wrapped_view"),
1657 MessageManager.getString("label.wrapped_view_no_edit"),
1658 JvOptionPane.WARNING_MESSAGE);
1662 if (seq < 0 || res < 0)
1667 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
1669 if ((sequence == null) || (res > sequence.getLength()))
1674 stretchGroup = av.getSelectionGroup();
1676 if (stretchGroup == null || !stretchGroup.contains(sequence, res))
1678 stretchGroup = av.getAlignment().findGroup(sequence, res);
1679 if (stretchGroup != null)
1681 // only update the current selection if the popup menu has a group to
1683 av.setSelectionGroup(stretchGroup);
1687 if (evt.isPopupTrigger()) // Mac: mousePressed
1694 * defer right-mouse click handling to mouseReleased on Windows
1695 * (where isPopupTrigger() will answer true)
1696 * NB isRightMouseButton is also true for Cmd-click on Mac
1698 if (SwingUtilities.isRightMouseButton(evt) && !Platform.isAMac())
1705 seqCanvas.cursorX = findColumn(evt);
1706 seqCanvas.cursorY = findSeq(evt);
1707 seqCanvas.repaint();
1711 if (stretchGroup == null)
1713 createStretchGroup(res, sequence);
1716 if (stretchGroup != null)
1718 stretchGroup.addPropertyChangeListener(seqCanvas);
1721 seqCanvas.repaint();
1724 private void createStretchGroup(int res, SequenceI sequence)
1726 // Only if left mouse button do we want to change group sizes
1727 // define a new group here
1728 SequenceGroup sg = new SequenceGroup();
1729 sg.setStartRes(res);
1731 sg.addSequence(sequence, false);
1732 av.setSelectionGroup(sg);
1735 if (av.getConservationSelected())
1737 SliderPanel.setConservationSlider(ap, av.getResidueShading(),
1741 if (av.getAbovePIDThreshold())
1743 SliderPanel.setPIDSliderSource(ap, av.getResidueShading(),
1746 // TODO: stretchGroup will always be not null. Is this a merge error ?
1747 // or is there a threading issue here?
1748 if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
1750 // Edit end res position of selected group
1751 changeEndRes = true;
1753 else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))
1755 // Edit end res position of selected group
1756 changeStartRes = true;
1758 stretchGroup.getWidth();
1763 * Build and show a pop-up menu at the right-click mouse position
1769 void showPopupMenu(MouseEvent evt)
1771 final int res = findColumn(evt);
1772 final int seq = findSeq(evt);
1773 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
1774 List<SequenceFeature> allFeatures = ap.getFeatureRenderer()
1775 .findFeaturesAtRes(sequence.getDatasetSequence(),
1776 sequence.findPosition(res));
1777 List<String> links = new ArrayList<>();
1778 for (SequenceFeature sf : allFeatures)
1780 if (sf.links != null)
1782 for (String link : sf.links)
1789 PopupMenu pop = new PopupMenu(ap, null, links);
1790 pop.show(this, evt.getX(), evt.getY());
1794 * Update the display after mouse up on a selection or group
1797 * mouse released event details
1799 * true if this event is happening after a mouse drag (rather than a
1802 public void doMouseReleasedDefineMode(MouseEvent evt, boolean afterDrag)
1804 if (stretchGroup == null)
1809 stretchGroup.removePropertyChangeListener(seqCanvas);
1811 // always do this - annotation has own state
1812 // but defer colourscheme update until hidden sequences are passed in
1813 boolean vischange = stretchGroup.recalcConservation(true);
1814 needOverviewUpdate |= vischange && av.isSelectionDefinedGroup()
1816 if (stretchGroup.cs != null)
1818 stretchGroup.cs.alignmentChanged(stretchGroup,
1819 av.getHiddenRepSequences());
1821 ResidueShaderI groupColourScheme = stretchGroup
1822 .getGroupColourScheme();
1823 String name = stretchGroup.getName();
1824 if (stretchGroup.cs.conservationApplied())
1826 SliderPanel.setConservationSlider(ap, groupColourScheme, name);
1828 if (stretchGroup.cs.getThreshold() > 0)
1830 SliderPanel.setPIDSliderSource(ap, groupColourScheme, name);
1833 PaintRefresher.Refresh(this, av.getSequenceSetId());
1834 ap.paintAlignment(needOverviewUpdate);
1835 needOverviewUpdate = false;
1836 changeEndRes = false;
1837 changeStartRes = false;
1838 stretchGroup = null;
1848 public void doMouseDraggedDefineMode(MouseEvent evt)
1850 int res = findColumn(evt);
1851 int y = findSeq(evt);
1853 if (wrappedBlock != startWrapBlock)
1858 if (stretchGroup == null)
1863 if (res >= av.getAlignment().getWidth())
1865 res = av.getAlignment().getWidth() - 1;
1868 if (stretchGroup.getEndRes() == res)
1870 // Edit end res position of selected group
1871 changeEndRes = true;
1873 else if (stretchGroup.getStartRes() == res)
1875 // Edit start res position of selected group
1876 changeStartRes = true;
1879 if (res < av.getRanges().getStartRes())
1881 res = av.getRanges().getStartRes();
1886 if (res > (stretchGroup.getStartRes() - 1))
1888 stretchGroup.setEndRes(res);
1889 needOverviewUpdate |= av.isSelectionDefinedGroup();
1892 else if (changeStartRes)
1894 if (res < (stretchGroup.getEndRes() + 1))
1896 stretchGroup.setStartRes(res);
1897 needOverviewUpdate |= av.isSelectionDefinedGroup();
1901 int dragDirection = 0;
1907 else if (y < oldSeq)
1912 while ((y != oldSeq) && (oldSeq > -1)
1913 && (y < av.getAlignment().getHeight()))
1915 // This routine ensures we don't skip any sequences, as the
1916 // selection is quite slow.
1917 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1919 oldSeq += dragDirection;
1926 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1928 if (stretchGroup.getSequences(null).contains(nextSeq))
1930 stretchGroup.deleteSequence(seq, false);
1931 needOverviewUpdate |= av.isSelectionDefinedGroup();
1937 stretchGroup.addSequence(seq, false);
1940 stretchGroup.addSequence(nextSeq, false);
1941 needOverviewUpdate |= av.isSelectionDefinedGroup();
1950 mouseDragging = true;
1952 if ((scrollThread != null) && (scrollThread.isRunning()))
1954 scrollThread.setEvent(evt);
1958 void scrollCanvas(MouseEvent evt)
1962 if ((scrollThread != null) && (scrollThread.isRunning()))
1964 scrollThread.stopScrolling();
1965 scrollThread = null;
1967 mouseDragging = false;
1971 if (scrollThread == null)
1973 scrollThread = new ScrollThread();
1976 mouseDragging = true;
1977 scrollThread.setEvent(evt);
1982 // this class allows scrolling off the bottom of the visible alignment
1983 class ScrollThread extends Thread
1987 private volatile boolean threadRunning = true;
1989 public ScrollThread()
1994 public void setEvent(MouseEvent e)
1999 public void stopScrolling()
2001 threadRunning = false;
2004 public boolean isRunning()
2006 return threadRunning;
2012 while (threadRunning)
2016 if (mouseDragging && (evt.getY() < 0)
2017 && (av.getRanges().getStartSeq() > 0))
2019 av.getRanges().scrollUp(true);
2022 if (mouseDragging && (evt.getY() >= getHeight()) && (av
2023 .getAlignment().getHeight() > av.getRanges().getEndSeq()))
2025 av.getRanges().scrollUp(false);
2028 if (mouseDragging && (evt.getX() < 0))
2030 av.getRanges().scrollRight(false);
2032 else if (mouseDragging && (evt.getX() >= getWidth()))
2034 av.getRanges().scrollRight(true);
2041 } catch (Exception ex)
2049 * modify current selection according to a received message.
2052 public void selection(SequenceGroup seqsel, ColumnSelection colsel,
2053 HiddenColumns hidden, SelectionSource source)
2055 // TODO: fix this hack - source of messages is align viewport, but SeqPanel
2056 // handles selection messages...
2057 // TODO: extend config options to allow user to control if selections may be
2058 // shared between viewports.
2059 boolean iSentTheSelection = (av == source
2060 || (source instanceof AlignViewport
2061 && ((AlignmentViewport) source).getSequenceSetId()
2062 .equals(av.getSequenceSetId())));
2064 if (iSentTheSelection)
2066 // respond to our own event by updating dependent dialogs
2067 if (ap.getCalculationDialog() != null)
2069 ap.getCalculationDialog().validateCalcTypes();
2075 // process further ?
2076 if (!av.followSelection)
2082 * Ignore the selection if there is one of our own pending.
2084 if (av.isSelectionGroupChanged(false) || av.isColSelChanged(false))
2090 * Check for selection in a view of which this one is a dna/protein
2093 if (selectionFromTranslation(seqsel, colsel, hidden, source))
2098 // do we want to thread this ? (contention with seqsel and colsel locks, I
2101 * only copy colsel if there is a real intersection between
2102 * sequence selection and this panel's alignment
2104 boolean repaint = false;
2105 boolean copycolsel = false;
2107 SequenceGroup sgroup = null;
2108 if (seqsel != null && seqsel.getSize() > 0)
2110 if (av.getAlignment() == null)
2112 Cache.log.warn("alignviewport av SeqSetId=" + av.getSequenceSetId()
2113 + " ViewId=" + av.getViewId()
2114 + " 's alignment is NULL! returning immediately.");
2117 sgroup = seqsel.intersect(av.getAlignment(),
2118 (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
2119 if ((sgroup != null && sgroup.getSize() > 0))
2124 if (sgroup != null && sgroup.getSize() > 0)
2126 av.setSelectionGroup(sgroup);
2130 av.setSelectionGroup(null);
2132 av.isSelectionGroupChanged(true);
2137 // the current selection is unset or from a previous message
2138 // so import the new colsel.
2139 if (colsel == null || colsel.isEmpty())
2141 if (av.getColumnSelection() != null)
2143 av.getColumnSelection().clear();
2149 // TODO: shift colSel according to the intersecting sequences
2150 if (av.getColumnSelection() == null)
2152 av.setColumnSelection(new ColumnSelection(colsel));
2156 av.getColumnSelection().setElementsFrom(colsel,
2157 av.getAlignment().getHiddenColumns());
2160 av.isColSelChanged(true);
2164 if (copycolsel && av.hasHiddenColumns()
2165 && (av.getAlignment().getHiddenColumns() == null))
2167 System.err.println("Bad things");
2169 if (repaint) // always true!
2171 // probably finessing with multiple redraws here
2172 PaintRefresher.Refresh(this, av.getSequenceSetId());
2173 // ap.paintAlignment(false);
2176 // lastly, update dependent dialogs
2177 if (ap.getCalculationDialog() != null)
2179 ap.getCalculationDialog().validateCalcTypes();
2185 * If this panel is a cdna/protein translation view of the selection source,
2186 * tries to map the source selection to a local one, and returns true. Else
2193 protected boolean selectionFromTranslation(SequenceGroup seqsel,
2194 ColumnSelection colsel, HiddenColumns hidden,
2195 SelectionSource source)
2197 if (!(source instanceof AlignViewportI))
2201 final AlignViewportI sourceAv = (AlignViewportI) source;
2202 if (sourceAv.getCodingComplement() != av
2203 && av.getCodingComplement() != sourceAv)
2209 * Map sequence selection
2211 SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
2212 av.setSelectionGroup(sg);
2213 av.isSelectionGroupChanged(true);
2216 * Map column selection
2218 // ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
2220 ColumnSelection cs = new ColumnSelection();
2221 HiddenColumns hs = new HiddenColumns();
2222 MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs);
2223 av.setColumnSelection(cs);
2224 av.getAlignment().setHiddenColumns(hs);
2226 // lastly, update any dependent dialogs
2227 if (ap.getCalculationDialog() != null)
2229 ap.getCalculationDialog().validateCalcTypes();
2232 PaintRefresher.Refresh(this, av.getSequenceSetId());